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Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of `open' reaction-diffusion systems…
We present an atomistic study of heterogeneous nucleation in Ni employing transition path sampling, which reveals a template precursor-mediated mechanism of crystallization. Most notably, we find that the ability of tiny templates to modify…
Existing studies comparing individual-based models of growing cell populations and their continuum counterparts have mainly focused on homogeneous populations, in which all cells have the same phenotypic characteristics. However,…
The Flory-Huggins theory is a well-established lattice model that is commonly used to study the mixing of distinct chemical species. It can successfully predict phase separation phenomena in blends of incompatible materials. However, it is…
Localised patterns are often observed in models for dryland vegetation, both as peaks of vegetation in a desert state and as gaps within a vegetated state, known as `fairy circles'. Recent results from radial spatial dynamics show that…
Micropatterning techniques have become an important tool for the study of cell behavior in controlled microenvironments. As a consequence, several approaches for the creation of micropatterns have been developed in recent years. However,…
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…
The process of pattern formation for a multi-species model anchored on a time varying network is studied. A non homogeneous perturbation superposed to an homogeneous stable fixed point can amplify, as follows a novel mechanism of…
We study pattern-forming instabilities in reaction-advection-diffusion systems. We develop an approach based on Lyapunov-Bloch exponents to figure out the impact of a spatially periodic mixing flow on the stability of a spatially…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
Crystallization of supersaturated liquids usually starts by heterogeneous nucleation. Mounting evidence shows that even homogeneous nucleation in simple liquids takes place in two steps; first a dense amorphous precursor forms, and the…
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells.…
Spatiotemporal patterns are common in biological systems. For electrically-coupled cells previous studies of pattern formation have mainly used external forcing as the main bifurcation parameter. The purpose of this paper is to show that…
During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular…
The development of multicellular organisms proceeds through a series of morphogenetic and cell-state transitions, transforming homogeneous zygotes into complex adults by a process of self-organization. Many of these transitions are achieved…